The special feature of the program is that it can read large (only
limited
by available memory) sequences, which can be translated in a special
format,
the 3-frame nested translation. The 3-frame nested translation can be
compared
against a protein sequence. Thus identifications of sequence
similarities
are possible even in case of frameshifts (due to sequence errors), or
when
exons are in different reading frames.

A description of this program has appeared in the journal
Bioinformatics:
Thomas R. Bürglin (1998)
PPCMatrix: a PowerPC dotmatrix program to compare large genomic
sequences
against protein sequences.
Bioinformatics 14: 751-752.

The program is released on shareware basis. Current pricing is US$
35
(checks, personal checks, or money orders drawn on US banks, or cash),
55 Swiss Francs (checks on Swiss banks in Swiss Francs) or 50 Swiss
Francs
(cash). Commercial companies please enquire.

Registered users will obtain a copy of the program that allows up to
600 sequences to be loaded (subject to available memory limitations).
In
addition, full documentation of all features is provided. Registered
users
will also receive bug fixes automatically by email as attachments.

This download version is fully functional, but limited to 5
sequences
resident in memory. The archives are self-extracting. In addition to
the
program application, there are 2 files (xx.tables) which contain the
translation
tables and the matrixes and need to be in the same folder as the
application.
Furthermore, a README file is included. The program generates a
Preferences
file (PPCMatrix Prefs) in the same folder, if none is present.

It is inspired, an partially compatible (the pics stack files) with
the software from C. Thomas and J. White, see their Web
site.

It offers two special features: recording in 2 channels (so
fluorescence
can be interspersed within DIC stacks),
and correction of microscope stage slippage with an software controlled
drift correction.
The hardware setup consists of a) any DIC &
fluorscence
microscope.
b) an ASI MFC-1 Z-axis drive
and
and an SC-2 dual shutter controller
attached to the microscope.
c) a Sony DXC-950 camera.
d) a Macintosh PowerPC with serial port to control the camera and the
ASI
devices.
e) a Scion CG-7 PCI framegrabber.

The software that controls this setup consists of 2 components:

a) Simple4DRecord
macros, a set of macros for the Scion Image application that comes with
the framegrabber.
With this you record stacks, and 4D series.

Degoligo

Degoligo is a small C program that runs in the terminal window of Mac
Os X (tested under 10.3).
The purpose of the program is to determine the probability of a
degenerate oligonucleotide sequence under conditions of 0, 1, 2, 3, 4,
or 5 mismatches.
For example, a degenerate oligonucleotide sequence is AARTCGYRG.
This sequence is 9 nucleotides long, and 8 fold degenerate.
The probability of this sequence is 3.05176e-05, which is 1
: 32768.
Thus, every 32768 nucleotides in average, you will find a match of this
sequence in a genome (A,C,T,G are assumed to be equally represented
with 25% each). So, in C. elegans (100 Million bases) you will find
about 3051 matches to this degenerate oligo with 0 mismatches.
If mismatches are allowed (as can happen during hybridisation), then
matches will occur of course more often. Hence the program also
calculates the probabilities for up to 5 mismatches.
Download the program